I am not sure if I understand your question - the "matrix" you define with the E modulus corresponding to the response in the weakest direction. All the matrix material values have to be related to the full volume (sometimes this approach is called bulk modulus). In other words, if you have E modulus of the clay material, it would correspond to a full brick (no openings) if directly used for the base material. If you have measured the response in some experiment and relate the force/reaction to the full crossection (i.e., not subratcting the internal voids), you have exactly what you need to put into ATENA.

For the stronger directions, a possible way is to simply take the "full clay" parameters for the multilin. law and apply the real additional cross section ratio (total cross section in the direction - cross section already included in the matrix material).